Christian Meesters
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rupdecat.fediscience.org.ap.brid.gy
Christian Meesters
@rupdecat.fediscience.org.ap.brid.gy
62 followers 3 following 600 posts
PhD in Biophysics, Postdoc in Genetic Epidemiology, Detour in Industry, Currently: Computational Scientist (Life Science Support) HPC (NHR, University of […]

🌉 bridged from https://fediscience.org/@rupdecat on the fediverse by https://fed.brid.gy/
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rupdecat.fediscience.org.ap.brid.gy
@wikipathways @egonw

Next attempt. Just using these libs:

library(rWikiPathways)
library(XML)
library(dplyr)
library(igraph)
library(ggraph)
library(ggplot2)

Still need to polish and work on the colour scale, though. Honestly? I, considering my workload, I […]

[Original post on fediscience.org]
overlay plot of a wikipathway showing over- and under expressed genes in red, resp. blue.
December 15, 2025 at 9:17 AM
rupdecat.fediscience.org.ap.brid.gy
@tschfflr I compete with my yesterday's deeds. Not as nice, but tasty.
Weizensauerteigsonntagsbrötchen Der Sauerteig vorm Füttern. Ein Dinkeltoast Haferkokosplätzchen
December 8, 2025 at 10:51 AM
rupdecat.fediscience.org.ap.brid.gy
@egonw a few days ago, I updated bumped the #bioconda package of r-wikipathways to v1.30 . Thank you for this wonderful package!

Today, after quite some tinkering, I managed to overly differential expression results. This is not stable code, yet. The […]

[Original post on fediscience.org]
Result of an R-Script illustrating downregulation (shades of blue) in a Drosophila pathway. The dataset was small, the results not reliable, the biological interpretation not feasible.
December 5, 2025 at 6:10 PM
rupdecat.fediscience.org.ap.brid.gy
To highlight the accomplishment a screenshot. It shows a Snakemake data analysis workflow running on "my" HPC system. Or rather a tiny fraction of a not-so-demanding workflow. Job submission of single core programs, scripts, threaded programs, MPI-programs […]

[Original post on fediscience.org]
Screenshopt (just one part) of a Snakemake Workflow running on an HPC-Cluster. One line, indicating the automated partition selection, is highlighted.
November 26, 2025 at 8:51 AM
rupdecat.fediscience.org.ap.brid.gy
Just submitted a talk for FOSDEM (been invited). They asked to attach an icon-image for the talk. So I drew one. The compute racks are difficult to identify as such, but this is as far as my aquarelle skills go.

#snakemake #reproduciblecomputing #hpc
A worker Snake, symbolizing the Snakemake workflow system, carrying a box labelled "SLURM plugin". Grim Face. Dark cloud overhead, labelled "policy". Subtitle: Reproducible computing on HPC clusters against the odds - the Snakemake SLURM plugin
November 2, 2025 at 7:58 PM
rupdecat.fediscience.org.ap.brid.gy
I fooled myself the other day: Was coding with VSC and "confirmed" a suggestion by the lovely Copilot #ai. Little did I know that, some place else, it was creating a test to check for minutes lasting longer than 59 seconds. (The actual time for 60 seconds […]

[Original post on fediscience.org]
screenshot of a unit test code showing the need to test for seconds converted to seconds - actually, this only seems ridiculous. And a test converting a duration of 3600 seconds to 3600 which is ridiculous because the time format would then be 1:00:00.
October 7, 2025 at 6:53 AM
rupdecat.fediscience.org.ap.brid.gy
My first contribution to #bioconda - not much, a rather old software. Took a while ...
screenshot of a GitHub notification showing an icon indicating the merger of a pull request
October 1, 2025 at 7:31 AM
rupdecat.fediscience.org.ap.brid.gy
@BlumeEvolution

Ein Beispiel: Demonstrieren!

@oneofakindfiona.bsky.social
Klimademo Mainz, jetzt.
September 20, 2025 at 9:06 AM
rupdecat.fediscience.org.ap.brid.gy
And apparently, the workflow is running with this new `--slurm-qos` flag.
screenshot of a #Snakemake workflow in action.
September 9, 2025 at 6:36 PM
rupdecat.fediscience.org.ap.brid.gy
Today, we will continue with some bits of #python - no Jupyter: I prefer, if my students can code scripts because we will continue later with some #snakemake.

Just some basics: types, loops, conditionals, strings ...

Day 2 of a data analytics course in applied #bioinformatics on #hpc systems.

2/n
Screenshot of a Python script converting degrees Fahrenheit to Celsius - still a version with a hard-coded value.
September 9, 2025 at 5:44 AM
rupdecat.fediscience.org.ap.brid.gy
This morning: introduction to the shell, then how to work remotely (SSH, terminal multiplexer, scp, rsync, ...)

Day 1 of a data analytics course in applied #bioinformatics on #hpc systems.

1/n
Photo of a projector showing the mkdir command.
September 8, 2025 at 4:09 PM
rupdecat.fediscience.org.ap.brid.gy
Framapad as an alternative to Google Docs. The default setting seems to be French, but changing to another language is easy enough. Looks pretty good.

https://framapad.org/
Framapad Screenshot - generated without account or login.
September 7, 2025 at 8:47 AM
rupdecat.fediscience.org.ap.brid.gy
Just loops, string manipulations and lists. And I can demonstrate a Burrows-Wheeler-Transform!

#academicchatter #teaching #python
Simple python code to demonstrate a burrows wheeler transform. No optimal implementation! Rather, some dummy code.
September 6, 2025 at 5:46 PM
rupdecat.fediscience.org.ap.brid.gy
Soooooo close to finalize a paper ...

Alas, the Pareto principle still applies.

#academicchatter
Snakemake report - screenshot of a heatmap showing differential expression results for unknown loci. To the right, a splicing isoform analysis.
September 2, 2025 at 11:32 AM
rupdecat.fediscience.org.ap.brid.gy
Testing course accounts and realizing that your batch system is down. 😨

#hpc #teaching #academicchatter
Screenshot of a terminal showing non-working SLURM commands.
September 1, 2025 at 5:46 AM
rupdecat.fediscience.org.ap.brid.gy
Intermediate result:

#nescollab #hackathon #nanopub
nanopub publication create on the command line using a schema json as input
August 29, 2025 at 9:42 AM
rupdecat.fediscience.org.ap.brid.gy
Ok, wir brauchen dringend mehr Wissenschaftskommunikation!
Zeitschriftencover: ChatGPT kann alles!
August 26, 2025 at 11:38 AM
rupdecat.fediscience.org.ap.brid.gy
Praying Mantis
August 16, 2025 at 6:25 AM
rupdecat.fediscience.org.ap.brid.gy
Es tut so verdammt gut, ab und an zu erleben, dass man nicht alleine ist. Die Klimakrise ist jetzt und es nicht egal wie lange wir uns gegen #Ökologie, #KlimaSchutz und eine lebenswerte Welt sperren!
Lesung von Luisa Neubauer Mikroübergabe an Katja Diehl Sehr viele Leute, die mit demonstrieren
July 15, 2025 at 1:49 PM
rupdecat.fediscience.org.ap.brid.gy
On my way to Hamburg, #isc25. The place where #hpc folks gather to learn about some new hardware trends.

Luckily, I will meet some like minded people, too. Those concerned about #usebility , #teaching , #ReproducibleResearch and so on.
Slightly obstructed view from a 🚆 across the river Rhine. And a blurred castle in the background.
June 10, 2025 at 11:10 AM
rupdecat.fediscience.org.ap.brid.gy
#snakemake in a #tmux session on our #hpc cluster. It is time to start into the weekend! All I have to do is detach the session and leave.
Screenshot of a terminal showing a progressing Snakemake data analysis workflow. Apparently, analysis jobs are automatically submitted to the cluster, the progress so far: a mere 3 %.
June 6, 2025 at 12:26 PM
rupdecat.fediscience.org.ap.brid.gy
Man, this was hard.

Alas, the Pareto principle still applies.

#academicchatter
indicators of successful CI runners
June 3, 2025 at 5:25 PM
rupdecat.fediscience.org.ap.brid.gy
@BlumeEvolution

Wenn es einmal regnet, bemühen wir uns weiterhin alles Wasser im Schuss zu Tal zu führen. Land auf, Land ab gibt es Drainagesysteme gegen Staunässe. Feuchtwiesen? Ökosysteme, die kaum jemand noch kennt.

Änderung in Sicht? Kluges Wassermanagement voraus? Eher nicht.
Entwässerungsgraben überhalb der Schwalm. Nordhessen. Gerade wurden die letzten Büsche abgesägt. Es gibt keinen Schatten mehr.
May 18, 2025 at 9:15 AM
rupdecat.fediscience.org.ap.brid.gy
@mainz_de

Es ist natürlich schade, dass Nazis einladen und mit einer scheinbar harmlosen, alltäglichen Fragestellung Werbung für sich machen. Man kann davon ausgehen, dass auch hier wieder Stimmung gegen #verkehrswende und #KlimaSchutz gemacht wird. Ich […]

[Original post on fediscience.org]
Informationsveranstaltung der #AFD zum Thema "Tempo 30 - Wie geht es weiter?". Eingeladen auch der OB und die Verkehrsdezernentin der Stadt Mainz.
May 14, 2025 at 3:26 PM
rupdecat.fediscience.org.ap.brid.gy
As it seems, using Lego aesthetics is legally doubtful: https://www.lego.com/en-de/legal/notices-and-policies/fair-play?locale=en-de

How do I know? Well, some here might remember the wonderful image collection of Lego minifigures for research data management […]

[Original post on fediscience.org]
Chapter cover for a data analysis course. This image shows some running lego minifigures with a roadrunner in the same aesthetic, carrying a laptop. LEGO is a trademark of the LEGO Group, which does not sponsor, authorize or endorse this image collection.
May 14, 2025 at 8:09 AM